Is there a way to lock stacked UV Islands when running Pack Islands?
Ok, so this still might be of interest to some of you...
This method involves the use of Blender's Texture Atlas Addon. It's in Blender's default addon section but needs to be installed.

Scenario: 

Let's assume we have four objects. Two of these objects are exact copies of the other two objects. Let's call them original1, original2, copy1 and copy2.



Let's further assume that at least the originals are fully unwrapped. 

All four objects should use the same texture, while the copies of the originals should use the same UV space within this texture. 

Creating the Texture Atlas

Open a new view and change it to UV/Texture Editor. 

Select original1 and original2 in the 3D View window.

In the Properties Window go to the Render Panel and scroll down until you find "Texture Atlas". Click on the "+" Button to create a new Atlas. 



A new window "add Lightmap" will pop up where you can change the name (not necessary imho). Click "Ok" to create the Texture Atlas.

Under "Texture Atlas" click on "No_Unwrap", then click on "StartManualUnwrap". 



(You might want to change the resolution here, you also can create a new texture later on)

In the 3D View window tab into "Edit mode". Now both original1 and original2 got merged into one object temporarily, should be in edit mode and you should see their overlapping UVs in the UV/Image Editor. 



In the UV/Image Editor go to "UVs" -> "Pack Islands". You also might to rearrange the UVs to use the Texture space more efficiently. 



When you are finished with rearranging the UV islands, go to "Texture Atlas" and hit the "FinishManualUnwrap" button. 

 

Both original1 and copy1 are now separated objects again and you dropped out of edit mode. 

If you select original1/2 and tab into edit mode the respective UV islands show up in the UV/Image Editor.

Copying the UV maps

In Object Mode select copy1, then shift-select original1. In the 3D View Menu Go to "Object -> Make Links -> Transfer UV Maps". 



Select copy1, tab into edit mode and change the Texture in the UV/Texture Editor to the Texture Atlas/the same texture you are using for original1

If done correctly copy1's UV space should be exactly the same as original1's. 



(I merged original1 and original2 into one object in this picture to show that both share the same UV space)

Repeat for copy2.